POST_FATE.binaryMaps: Create binary maps for each Plant Functional Group for one...
In MayaGueguen/RFate: Vegetation modelling with the FATE model

Description Usage Arguments Details Value Author(s) See Also Examples

This script is designed to produce raster maps of PFG presence / absence for one (or several) specific FATE simulation year.

POST_FATE.binaryMaps(
  name.simulation,
  file.simulParam = NULL,
  years,
  method,
  method1.threshold = 0.05,
  method2.cutoff = NULL,
  opt.no_CPU = 1
)

`name.simulation`	a `string` corresponding to the main directory or simulation name of the `FATE` simulation
`file.simulParam`	default `NULL`. A `string` corresponding to the name of a parameter file that will be contained into the `PARAM_SIMUL` folder of the `FATE` simulation
`years`	an `integer`, or a `vector` of `integer`, corresponding to the simulation year(s) that will be used to extract PFG abundance maps
`method`	an `integer` to choose the transformation method : `1` (relative abundance) or `2` (optimizing TSS) (see `Details`)
`method1.threshold`	default `0.05`. If `method = 1`, minimum relative abundance required for each PFG to be considered as present in the concerned pixel
`method2.cutoff`	default `NULL`. If `method = 2`, a `data.frame` with 3 columns : `year`, `PFG`, `cutoff` (see `Details`)
`opt.no_CPU`	(optional) default `1`. The number of resources that can be used to parallelize the `unzip/zip` of raster files

This function allows to obtain, for a specific FATE simulation and a specific parameter file within this simulation, raster maps of PFG presence / absence.

For each PFG and each selected simulation year, raster maps are retrieved from the results folder ABUND_REL_perPFG_allStrata and lead to the production of as many maps as those found :

1 fixed threshold

relative abundance maps are transformed into binary maps according to the threshold given by method1.threshold :

abund\_rel_{\text{ PFG}_i} > \text{method1.threshold} \;\; \Leftrightarrow \;\; 1

2 optimizing TSS

relative abundance maps are transformed into binary maps according to the cutoff found with the POST_FATE.graphic_validationStatistics function :

abund\_rel_{\text{ PFG}_i} > \text{method2.cutoff}_{\text{ PFG}_i} \;\; \Leftrightarrow \;\; 1

Binary maps per stratum are obtained by multiplying raster maps from ABUND_perPFG_perStrata folder by corresponding raster maps from BIN_perPFG_allStrata folder.

It requires that the POST_FATE.relativeAbund function has been run and that the folder ABUND_REL_perPFG_allStrata exists.
If method = 2, it requires that the POST_FATE.graphic_validationStatistics function has been run.

These binary raster files can then be used by other functions :

to produce graphics of PFG modelled presence vs PFG Habitat Suitability maps
(see POST_FATE.graphic_mapPFGvsHS)

Two folders are created :

‘BIN_perPFG _allStrata’: containing presence / absence raster maps for each PFG across all strata
‘BIN_perPFG _perStrata’: containing presence / absence raster maps for each PFG for each stratum

Maya Guéguen

POST_FATE.relativeAbund, POST_FATE.graphic_validationStatistics .getCutoff, POST_FATE.graphic_mapPFGvsHS

                                                        
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MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.